NBIS (National Bioinformatics Infrastructure Sweden) is a distributed national research infrastructure supported by the Swedish Research Council (Vetenskapsrådet), Science for Life Laboratory, all major Swedish universities and the Knut and Alice Wallenberg Foundation, providing state-of-the-art bioinformatics to the Swedish researchers in Life Sciences. NBIS is also the Swedish contact point to the European infrastructure for biological information ELIXIR.
Health & Medicine
National Bioinformatics Infrastructure Sweden - NBIS
The Challenge
NBIS is predominantly offering bioinformatics support in various projects, depending on the user needs. In the projects, the NBIS persons are working close to the research group, and they spend part of their time teaching the users in order to propagate the bioinformatics knowledge. Present NBIS staff has expertise in protein bioinformatics, mass spectrometry (MS), next-generation sequencing (NGS), large-scale data handling and integration, metagenomics, systems biology, biostatistics and RNAseq.
More specifically, NBIS offers:
- High-quality training programs aimed at the Swedish Life Science research community provide a standard to follow when handling and analysing bioinformatics data. The training follows up-to-date best practices for effective teaching, using Open and FAIR training materials. Moreover, our training is inclusive and meets the needs of the research community in terms of accessibility.
- Infrastructure and tools for bioinformatics analyses in order to facilitate these analyses for the users.
The Solution
The NBIS compute and storage facility hosted at Uppsala Multidisciplinary Center for Advanced Computational Science (SNIC-UPPMAX) provides high-performance computing and storage resources, maintain relevant bioinformatics software and data, and offer associated user support. Starting from December 2015, EGI is contributing with additional pledged resources to allow the bioinformatics community to use Cloud Computing and Online Storage services needed to develop portals for Life Science researchers worldwide.
The NBIS toolkits are based on:
- A web page front end to the services exposed to the users.
- A backend consisting of a variety of software and scripts.
- The EGI computing and storage resources such as the EGI Cloud Compute and the EGI Online Storage to host some of the NBIS portals.
Impact
Pconsc3.net
239 active users over the last 6 years
ProQ3
1,677 active users over the last 6 years
BOCTOPUS
2,464 active users over the last 6 years
subcons
427 active users over the last 6 years
topcons2
28,634 active users over the last 6 years
scampi2
1,056 active users over the last 6 years
>1,513,594 Millions of (Cloud) CPU Hours
over the last 6 years
260 VMs
instantiated in the EGI Federated Cloud infrastructure over the last 6 years
2M (Cloud) CPU Hours
over the last two years
Highlights
NBIS Toolkits
Check the resources available in the NBIS toolkits!
NBIS Training
NBIS offers a spectrum of training events, ranging from introductory classes to advanced workshops, e.g. on R and Python programming, general high-throughput sequencing data analysis, RNA-seq and single-cell RNA-seq.
NBIS also provides a 2-year advisory program for PhD students interested in having a bioinformatics expert as an additional mentor.
Nanjiang Shu, Deputy Head of System Development at NBIS, says:
“We appreciate the robust service provided by EGI during the past few years of collaboration. I believe more and more researchers will benefit from the work powered by the services provided by EGI.”
Participating Partners
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